Spiers, who has led the CPRE since 2004, will succeed Matthew Spencer, who left the Green Alliance in September to become director of campaigns, policy and influencing at Oxfam GB.
Before joining the CPRE, Spiers was chief executive of the credit union trade association Abcul, and was a Labour and Co-operative MEP for London South East between 1994 and 1999.
Spiers said he would be taking up the role at the Green Alliance, which aims to promote sustainable development, at a pivotal time for the British environment.
"Brexit is a once-in-a-generation chance to strengthen environmental protection, improve countryside quality and set a path to a low carbon and resource-efficient future," he said.
"But it also carries with it great risks. Green Alliance’s work with other green and civil society groups and progressive businesses will be essential to building a vision of the sort of country we want to be, and ensuring the best possible environmental outcomes."
Su Sayer, chair of the CPRE, said Spiers had been "an inspirational chief executive".
Spiers, who will take up his new role in June, said in a letter published in Third Sector last year that think tanks should be put under greater pressure to say where they get their funding.
A spokeswoman for the Green Alliance said the charity would not disclose how much Spiers would be paid.